cbcb_filter_counts: Filter low-count genes from a data set using cpm data and a...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Filter low-count genes from a data set using cpm data and a threshold.

Description

This was a function written by Kwame Okrah and perhaps also Laura Dillon to remove low-count genes. It drops genes based on a cpm threshold and number of samples.

Usage

cbcb_filter_counts(count_table, threshold = 1, min_samples = 2, libsize = NULL)

Arguments

count_table	Data frame of (pseudo)counts by sample.
threshold	Lower threshold of counts for each gene.
min_samples	Minimum number of samples.
libsize	Table of library sizes.

Value

Dataframe of counts without the low-count genes.

See Also

[edgeR]

Examples

## Not run: 
 filtered_table <- cbcb_filter_counts(count_table)

## End(Not run)

elsayed-lab/hpgltools documentation built on April 8, 2024, 1:30 a.m.